I definitely finished the era as I was shown the screen which shows you which resource you unlocked for each achievement. It's not the resource itself, as after completing that task a 2nd time it has now unlocked.

Actually I have a theory about this - just discovered that I was in offline mode in Steam. It is possible that achievements aren't persisted when Steam is offline.

If this is what's happening then I'd suggest that it would be better if the game locally caches achievements if it discovers it's offline and does a re-sync with Steam next time it's online, adding unlocks to Steam that aren't there and also adding unlocks to the local game from steam.